While this may not be conclusive, I have a theory of why this is the case. Looking at all the Legendary and Mythical Pokémon in Pokémon Mystery Dungeon: Explorers of Sky and all the previous games, I discovered all Legendary and Mythical Pokemon with a signature item, and discovered a pattern. All of these Pokémon have 1 signature Item. Palkia, Dialga, Articuno, Moltres, they all have 1 signature item (Except for Phione, but it's status is debated anyway). So, my theory is that they only gave Shaymin 1 signature item because they wanted to keep to the pattern of Legendary and Mythical Pokemon only having 1 signature item.